Tools for working with genomic and high throughput sequencing data.
Group: Utilities
Updates the contig names in columns of a delimited data file (e.g. CSV, TSV).
The name of each sequence must match one of the names (including aliases) in the given sequence dictionary. The
new name will be the primary (non-alias) name in the sequence dictionary. Use --skip-missing to ignore lines
where a contig name could not be updated (i.e. missing from the sequence dictionary).
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | FilePath | Input delimited data file. | Required | 1 | |
| dict | d | PathToSequenceDictionary | The path to the sequence dictionary with contig aliases. | Required | 1 | |
| columns | c | Int | The column indices for the contig names (0-based). | Required | Unlimited | |
| delimiter | T | Char | The delimiter | Optional | 1 | \t |
| comment | H | String | Treat lines with this starting string as comments (always printed) | Optional | 1 | # |
| output | o | FilePath | Output delimited data file. | Required | 1 | |
| output-first-num-lines | n | Int | Output the first N lines as-is (always printed). |
Optional | 1 | 0 |
| skip-missing | Boolean | Skip lines where a contig name could not be updated (i.e. missing from the sequence dictionary). | Optional | 1 | false | |
| sort-order | s | SortOrder | Sort the output based on the following order. | Optional | 1 | Unsorted |
| contig | Int | The column index for the contig (0-based) for sorting. Use the first column if not given. | Optional | 1 | ||
| position | Int | The column index for the genomic position (0-based) for sorting by coordinate. | Optional | 1 | ||
| max-objects-in-ram | Int | The maximum number of objects to store in memory | Optional | 1 | 1000000 |